Git Flow when coding for blender
You work with source code in the src folder of the cloned blender repo directly. If there is no project file for the IDE included (in your case the Visual Studio Solution) you need to create one and set it up to use this src folder.
Fortunately, Visual Studio offers support for git, so all you have to do is create a new Visual Studio Solution and set up git and the blender repo. Then you can track your changes and do the versioning in Visual Studio.
Of course you can still use the git command line but the source files stay in the src folder. Git handles the changes and keeps track of them. The repo itself with all versions and changes is usually stored in a folder named &quot;.git&quot; inside of the main folder.
Hope that helps.